Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 19
Found at i:2806259 original size:4 final size:4
Alignment explanation
Indices: 2806250--2806291 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
2806240 TATGAGAAAC
* * *
2806250 AATA AATA AATG AATG AATG AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
2806292 CAATGGTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:2807874 original size:15 final size:15
Alignment explanation
Indices: 2807854--2807883 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2807844 TAATCGTCTA
2807854 CTTTCGAGTTGTTTT
1 CTTTCGAGTTGTTTT
2807869 CTTTCGAGTTGTTTT
1 CTTTCGAGTTGTTTT
2807884 ACACCCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.20, T:0.60
Consensus pattern (15 bp):
CTTTCGAGTTGTTTT
Found at i:2829892 original size:16 final size:16
Alignment explanation
Indices: 2829871--2829905 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2829861 ACACCATCCA
2829871 AAACCCAAATTGAAAC
1 AAACCCAAATTGAAAC
2829887 AAACCCAAATTGAAAC
1 AAACCCAAATTGAAAC
2829903 AAA
1 AAA
2829906 TCAAGAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (16 bp):
AAACCCAAATTGAAAC
Found at i:2837117 original size:35 final size:33
Alignment explanation
Indices: 2837071--2837144 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 33
2837061 AAAACAGTCC
*
2837071 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAA--AAT
*
2837106 TCAATTTCATTCTAAACCCTAAATTCCAAAAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAAT
2837139 TCAATT
1 TCAATT
2837145 AAATTCAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 9 0.24
35 28 0.76
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.35
Consensus pattern (33 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAAAT
Found at i:2837677 original size:126 final size:120
Alignment explanation
Indices: 2837518--2837767 Score: 340
Period size: 123 Copynumber: 2.0 Consensus size: 120
2837508 TTCAGTCTTT
* * **
2837518 ATTATTTATATAATCAATTTGGTTCTAAATTAATAGAA-TTAATAAATTAATCATTTAATTAGGA
1 ATTATTTATATAATCAATTTGGTCCTAAATTAATAAAATTTAATAAATTAATCATTTAACCAGGA
* *
2837582 TCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
66 --T--CATGTGTTAACACATGATCATGACACATGTCATTGGT-ACACATGTCACCACCTA
*
2837642 ATTATTTATATGCTATCAATTTGGTCCTAAATTAATAAAATTTAATAAATTAATCATTTAACCAG
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAATAAAATTTAATAAATTAATCATTTAACCAG
* * *
2837707 GATCATGTGTTAACACATGATCATGATATATGTTATTGGTACACATGTCACCACCTA
64 GATCATGTGTTAACACATGATCATGACACATGTCATTGGTACACATGTCACCACCTA
2837764 ATTA
1 ATTA
2837768 GAAGAAAATT
Statistics
Matches: 113, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
122 21 0.19
123 32 0.28
124 11 0.10
125 1 0.01
126 24 0.21
127 24 0.21
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (120 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAATAAAATTTAATAAATTAATCATTTAACCAGGA
TCATGTGTTAACACATGATCATGACACATGTCATTGGTACACATGTCACCACCTA
Found at i:2838122 original size:28 final size:26
Alignment explanation
Indices: 2838091--2838151 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2838081 AGTTGATACA
*
2838091 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTT-AAA-AATAAATTTAAGAATT
* * *
2838119 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAAGAATT
2838145 ATATTTT
1 ATATTTT
2838152 TCATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.69
27 2 0.07
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAAGAATT
Found at i:2838250 original size:15 final size:16
Alignment explanation
Indices: 2838226--2838262 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2838216 TTTAATTTCT
2838226 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
2838240 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
2838256 TGATTCA
1 T-ATTCA
2838263 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:2841553 original size:255 final size:255
Alignment explanation
Indices: 2841102--2841611 Score: 1020
Period size: 255 Copynumber: 2.0 Consensus size: 255
2841092 AAGATGAGGC
2841102 ATACATAAACAAAACCAGTAAAATCAAAAGATAAACATTAATCAACCATTAAAACAAAGTTTTCA
1 ATACATAAACAAAACCAGTAAAATCAAAAGATAAACATTAATCAACCATTAAAACAAAGTTTTCA
2841167 AGCATCCATCAAATGAACCCCACCAAATTTAGCTTAGTTCATGGCGGGGTTCGAATAAACCATGG
66 AGCATCCATCAAATGAACCCCACCAAATTTAGCTTAGTTCATGGCGGGGTTCGAATAAACCATGG
2841232 AAAATATCCAATCATTCATTCAACCAAACAACCCAAATAAGTTTTCAATATTTAAACAATGGAGC
131 AAAATATCCAATCATTCATTCAACCAAACAACCCAAATAAGTTTTCAATATTTAAACAATGGAGC
2841297 AAAGTTTGGAGAAGAAAACACTCGATGTGCACGGCTGGCGCTTTCTCAAACCACCATGAA
196 AAAGTTTGGAGAAGAAAACACTCGATGTGCACGGCTGGCGCTTTCTCAAACCACCATGAA
2841357 ATACATAAACAAAACCAGTAAAATCAAAAGATAAACATTAATCAACCATTAAAACAAAGTTTTCA
1 ATACATAAACAAAACCAGTAAAATCAAAAGATAAACATTAATCAACCATTAAAACAAAGTTTTCA
2841422 AGCATCCATCAAATGAACCCCACCAAATTTAGCTTAGTTCATGGCGGGGTTCGAATAAACCATGG
66 AGCATCCATCAAATGAACCCCACCAAATTTAGCTTAGTTCATGGCGGGGTTCGAATAAACCATGG
2841487 AAAATATCCAATCATTCATTCAACCAAACAACCCAAATAAGTTTTCAATATTTAAACAATGGAGC
131 AAAATATCCAATCATTCATTCAACCAAACAACCCAAATAAGTTTTCAATATTTAAACAATGGAGC
2841552 AAAGTTTGGAGAAGAAAACACTCGATGTGCACGGCTGGCGCTTTCTCAAACCACCATGAA
196 AAAGTTTGGAGAAGAAAACACTCGATGTGCACGGCTGGCGCTTTCTCAAACCACCATGAA
2841612 TGGCTATAGC
Statistics
Matches: 255, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 255 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (255 bp):
ATACATAAACAAAACCAGTAAAATCAAAAGATAAACATTAATCAACCATTAAAACAAAGTTTTCA
AGCATCCATCAAATGAACCCCACCAAATTTAGCTTAGTTCATGGCGGGGTTCGAATAAACCATGG
AAAATATCCAATCATTCATTCAACCAAACAACCCAAATAAGTTTTCAATATTTAAACAATGGAGC
AAAGTTTGGAGAAGAAAACACTCGATGTGCACGGCTGGCGCTTTCTCAAACCACCATGAA
Found at i:2849050 original size:24 final size:21
Alignment explanation
Indices: 2849015--2849057 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2849005 GGCTCATTCT
*
2849015 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2849038 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2849058 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2860295 original size:21 final size:21
Alignment explanation
Indices: 2860253--2860295 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2860243 TTCAATTTTA
**
2860253 ATTGAATTTTATATTTAATAT
1 ATTGAATTTTATAAATAATAT
* *
2860274 ATTGTATTTTATAAATACTAT
1 ATTGAATTTTATAAATAATAT
2860295 A
1 A
2860296 AAATTCTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTGAATTTTATAAATAATAT
Found at i:2862175 original size:38 final size:36
Alignment explanation
Indices: 2862124--2862198 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 36
2862114 TGACTTGTTC
*
2862124 AAAATTAACATGTGGGATAAAGATCATGTCCGGGTAGG
1 AAAATAAACATGTGGGATAAAGATCATGT--GGGTAGG
* * *
2862162 AAAATAAACATGTGGGGTAGATATCATGTGGGTAGG
1 AAAATAAACATGTGGGATAAAGATCATGTGGGTAGG
2862198 A
1 A
2862199 CTTTTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 8 0.24
38 25 0.76
ACGTcount: A:0.37, C:0.08, G:0.31, T:0.24
Consensus pattern (36 bp):
AAAATAAACATGTGGGATAAAGATCATGTGGGTAGG
Found at i:2864575 original size:35 final size:35
Alignment explanation
Indices: 2864513--2864590 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
2864503 TTTTGCAGCA
2864513 TCTTGTTTGAACTTGTTTTTTAAACTTTCTCATATT
1 TCTT-TTTGAACTTGTTTTTTAAACTTTCTCATATT
*
2864549 TCTTTTTGTAACTTG-TTTTTGAACTTTCTCATATT
1 TCTTTTTG-AACTTGTTTTTTAAACTTTCTCATATT
2864584 TCTTTTT
1 TCTTTTT
2864591 ATAAGGATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 30 0.75
36 10 0.25
ACGTcount: A:0.17, C:0.14, G:0.08, T:0.62
Consensus pattern (35 bp):
TCTTTTTGAACTTGTTTTTTAAACTTTCTCATATT
Found at i:2865265 original size:99 final size:99
Alignment explanation
Indices: 2865102--2865304 Score: 309
Period size: 99 Copynumber: 2.1 Consensus size: 99
2865092 TTATAATATT
* * * *
2865102 ATATATATATAATAAAGCTTAAGTTGTCCCTCTAGAGTAATTGGTTAAATGCCCCAATTTTATGG
1 ATATTTATACAATAAAGCTTAAGCTGTCCCTCTAGAGTAATTGGTTAAATGCCCCAACTTTATGG
*
2865167 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAGCCTGATAAAGGTGATTATA
* * *
2865201 ATATTTATACAATAAAGCTTGAGCTGTCCCTCTAGAGTAATTGGTTAAACT-CTCCGACTTTATG
1 ATATTTATACAATAAAGCTTAAGCTGTCCCTCTAGAGTAATTGGTTAAA-TGCCCCAACTTTATG
*
2865265 GATAAGATTCAACTAGCCTGATAAATGTGATTATA
65 GATAAGATTCAACTAGCCTGATAAAGGTGATTATA
2865300 ATATT
1 ATATT
2865305 AAGCTGTCCC
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
99 93 0.99
100 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (99 bp):
ATATTTATACAATAAAGCTTAAGCTGTCCCTCTAGAGTAATTGGTTAAATGCCCCAACTTTATGG
ATAAGATTCAACTAGCCTGATAAAGGTGATTATA
Found at i:2867952 original size:26 final size:26
Alignment explanation
Indices: 2867916--2867972 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2867906 TCGTTCGACC
*
2867916 ATATTATATAATATGTTATCTA-TATT
1 ATATAATATAA-ATGTTATCTATTATT
* *
2867942 ATATAATATAAATGTTTTTTATTATT
1 ATATAATATAAATGTTATCTATTATT
2867968 ATATA
1 ATATA
2867973 TACATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (26 bp):
ATATAATATAAATGTTATCTATTATT
Found at i:2868014 original size:21 final size:20
Alignment explanation
Indices: 2867960--2868015 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 20
2867950 TAAATGTTTT
2867960 TTATTATTATATATACATATA
1 TTATTATTAT-TATACATATA
2867981 TTA-TATTAAATTATACATATTA
1 TTATTATT--ATTATACATA-TA
2868003 TTATTATTATTAT
1 TTATTATTATTAT
2868016 TATAATGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.13
21 16 0.52
22 7 0.23
23 4 0.13
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTATTATTATACATATA
Found at i:2870183 original size:37 final size:37
Alignment explanation
Indices: 2870142--2870310 Score: 180
Period size: 37 Copynumber: 4.5 Consensus size: 37
2870132 TACAATATTG
* *
2870142 TATTTCAATTGAATACAAATTCGTAATAATATATTCA
1 TATTTCAATTGAATATAAATTCATAATAATATATTCA
* **
2870179 TATTTTAATTGAATATAAATTTACAT-ATAATATATTTG
1 TATTTCAATTGAATATAAA-TT-CATAATAATATATTCA
** * *
2870217 TATTT-AATCAAATATAAATTTATAAATAATATATTCC
1 TATTTCAATTGAATATAAATTCAT-AATAATATATTCA
**
2870254 TATTTCAATCAAATATAAATTCATAATAATATATTCA
1 TATTTCAATTGAATATAAATTCATAATAATATATTCA
* *
2870291 CATTTTAATTGAATATAAAT
1 TATTTCAATTGAATATAAAT
2870311 CTTTAAATAA
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
35 2 0.02
36 2 0.02
37 71 0.64
38 34 0.31
39 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TATTTCAATTGAATATAAATTCATAATAATATATTCA
Found at i:2870298 original size:75 final size:75
Alignment explanation
Indices: 2870166--2870322 Score: 185
Period size: 75 Copynumber: 2.1 Consensus size: 75
2870156 ACAAATTCGT
* ** ***
2870166 AATAATATATTCATATTTTAATTGAATATAAATTTACATATAATATATTTGTATTTAATCAAATA
1 AATAATATATTCATATTTCAATCAAATATAAATTTACATATAATATATTCACATTTAATCAAATA
2870231 TAAAT-TTATA
66 TAAATCTT-TA
* **
2870241 AATAATATATTCCTATTTCAATCAAATATAAA-TT-CATAATAATATATTCACATTTTAATTGAA
1 AATAATATATTCATATTTCAATCAAATATAAATTTACAT-ATAATATATTCACA-TTTAATCAAA
2870304 TATAAATCTTTA
64 TATAAATCTTTA
2870316 AATAATA
1 AATAATA
2870323 GAATATTATC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
73 3 0.04
74 13 0.19
75 52 0.74
76 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (75 bp):
AATAATATATTCATATTTCAATCAAATATAAATTTACATATAATATATTCACATTTAATCAAATA
TAAATCTTTA
Found at i:2871817 original size:28 final size:28
Alignment explanation
Indices: 2871774--2871925 Score: 84
Period size: 28 Copynumber: 5.3 Consensus size: 28
2871764 TCAATTTTAA
*
2871774 AAAATATTT-TATTATTATTTTTAATTT
1 AAAATATTTATTTTATTATTTTTAATTT
* *
2871801 AAAATATTTATTTTATTCTTATCTTAACTT
1 AAAATATTTATTTTATTATT-T-TTAATTT
* *
2871831 AGAAATATATTAATTT-TTA-TTTTAACTTA
1 A-AAATAT-TTATTTTATTATTTTTAA-TTT
*
2871860 AAAATATATT-TATTT-TTATTTTAAATTTT
1 AAAATAT-TTAT-TTTATTATTTTTAA-TTT
* *
2871889 AAAA-ATATAGTTTATT-TTGTCTTAATTT
1 AAAATATTTATTTTATTATT-T-TTAATTT
2871917 AAATATATT
1 AAA-ATATT
2871926 CCAAATATAT
Statistics
Matches: 96, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
27 15 0.16
28 38 0.40
29 19 0.20
30 10 0.10
31 8 0.08
32 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (28 bp):
AAAATATTTATTTTATTATTTTTAATTT
Found at i:2871895 original size:58 final size:61
Alignment explanation
Indices: 2871746--2871906 Score: 156
Period size: 58 Copynumber: 2.7 Consensus size: 61
2871736 AAACCATTAA
* * * * *
2871746 ATATATTTTATTC-TAGACTCAATTTTAAAAA-ATATTTTATTATTATTTTTAATTTAAAAT
1 ATATATTTTATTCTTA-TCTTAATTTTAAAAATATAGTTTATTTTTATTTTTAACTTAAAAT
* * * *
2871806 ATTTATTTTATTCTTATCTTAA-CTTAGAAATATA-TTAATTTTTA-TTTTAACTTAAAA-
1 ATATATTTTATTCTTATCTTAATTTTAAAAATATAGTTTATTTTTATTTTTAACTTAAAAT
* *
2871863 ATATA-TTTATTTTTATTTTAAATTTTAAAAATATAGTTTATTTT
1 ATATATTTTATTCTTATCTT-AATTTTAAAAATATAGTTTATTTT
2871907 GTCTTAATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
56 12 0.15
57 6 0.07
58 22 0.27
59 21 0.26
60 19 0.23
61 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (61 bp):
ATATATTTTATTCTTATCTTAATTTTAAAAATATAGTTTATTTTTATTTTTAACTTAAAAT
Found at i:2871919 original size:58 final size:57
Alignment explanation
Indices: 2871744--2871924 Score: 154
Period size: 58 Copynumber: 3.1 Consensus size: 57
2871734 TAAAACCATT
* *
2871744 AAATATATTTTATTC-TAGACTCAATTTTAAAAA-ATATTTTATTATTATTTTTAATTTAA
1 AAATATATTTTATTCTTA-TCTTAATTTTAAAAATATA-TTTATT-TTA-TTTTAATTTAA
* * * * *
2871803 AATATTTATTTTATTCTTATCTTAA-CTTAGAAATATATTAATTTTTATTTTAACTTAA
1 AA-ATATATTTTATTCTTATCTTAATTTTAAAAATATATTTA-TTTTATTTTAATTTAA
* * * *
2871861 AAATATA-TTTATTTTTATTTTAAATTTTAAAAATATAGTTTATTTTGTCTTAATTTAA
1 AAATATATTTTATTCTTATCTT-AATTTTAAAAATATA-TTTATTTTATTTTAATTTAA
*
2871919 ATATAT
1 AAATAT
2871925 TCCAAATATA
Statistics
Matches: 98, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
56 12 0.12
57 6 0.06
58 40 0.41
59 17 0.17
60 21 0.21
61 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (57 bp):
AAATATATTTTATTCTTATCTTAATTTTAAAAATATATTTATTTTATTTTAATTTAA
Found at i:2871939 original size:87 final size:86
Alignment explanation
Indices: 2871773--2871941 Score: 193
Period size: 87 Copynumber: 2.0 Consensus size: 86
2871763 CTCAATTTTA
* * *
2871773 AAAAATATTTTATTATTATTTTTAATTTAAAATATTTATTTTATTCTTATCTTAACTTAGAAATA
1 AAAAATATTTTATTATTATTTTAAATTTAAAATATATAGTTTATTCTTATCTTAACTTAGAAATA
* *
2871838 TATTAATTTTTATTTTAACTT
66 TATTAATATATATTTTAACTT
* * *
2871859 AAAAATATATTTATTTTTATTTTAAATTTTAAAA-ATATAGTTTATT-TTGTCTTAA-TT-TAAA
1 AAAAATAT-TTTATTATTATTTTAAA-TTTAAAATATATAGTTTATTCTTATCTTAACTTAGAAA
2871920 TATATTCCAAATATATATTTTA
64 TATATT---AATATATATTTTA
2871942 TTCCTATATT
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
84 9 0.13
85 2 0.03
86 16 0.23
87 36 0.51
88 7 0.10
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (86 bp):
AAAAATATTTTATTATTATTTTAAATTTAAAATATATAGTTTATTCTTATCTTAACTTAGAAATA
TATTAATATATATTTTAACTT
Found at i:2871968 original size:30 final size:30
Alignment explanation
Indices: 2871932--2871997 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
2871922 TATTCCAAAT
*
2871932 ATATATTTTATTCCTA-TATTAGCTTATTAA
1 ATATATTTTATTCCTACTA-TAACTTATTAA
*
2871962 ATATATTTTATTCTTACTATAACTTATTAA
1 ATATATTTTATTCCTACTATAACTTATTAA
2871992 ATATAT
1 ATATAT
2871998 GTTAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATTTTATTCCTACTATAACTTATTAA
Found at i:2873258 original size:264 final size:264
Alignment explanation
Indices: 2872788--2873313 Score: 908
Period size: 264 Copynumber: 2.0 Consensus size: 264
2872778 AAAACTATAC
* *
2872788 TAAACTTTAAACTTTTATTAACACAAAAGTTATACATACATAATTGAGTTCGAAACATTACAAAA
1 TAAACTTTAAACTTTTATTAACAAAAAAGTCATACATACATAATTGAGTTCGAAACATTACAAAA
2872853 TTCATCAGAGCATACATAAATAACACCTTTGTACATGCCAACTATTTGACTCAACAAAATACCTA
66 TTCATCAGAGCATACATAAATAACACCTTTGTACATGCCAACTATTTGACTCAACAAAATACCTA
* * *
2872918 TTGTGTATTTACTTCTGATCTGATCTTCGAGTGAAACTATGATGCTCTGTAAATTCTAATCTTGA
131 CTGTGTATTTACTTCTGATCTGATCTTCAAGTGAAACTATGATGCTCTGAAAATTCTAATCTTGA
* * *
2872983 TCCTCTTGCTCCTCTGAACCTATGTGTAAAAACATTTACATGCTAAGTCATAGACTTAGTGAAGC
196 TCCTCTTGCTCCTCTGAACCTACGTGTAAAAACACTTACACGCTAAGTCATAGACTTAGTGAAGC
2873048 ACTT
261 ACTT
* *
2873052 TAAACTTTAAACTTTTATTAACAAAAAAGTCATATATACATAATTGAGTTCGAAACGTTACAAAA
1 TAAACTTTAAACTTTTATTAACAAAAAAGTCATACATACATAATTGAGTTCGAAACATTACAAAA
* * *
2873117 TTGATCAGAGCATACATAAATTACACCTTTGTACATGCCAACTATTTGACTCCACAAAATACCTA
66 TTCATCAGAGCATACATAAATAACACCTTTGTACATGCCAACTATTTGACTCAACAAAATACCTA
*
2873182 CTGTGTATTTACTTCTGATCTGATCTTCAAGTGAAACTATGATGCTCTGAAAATTCTATTCTTGA
131 CTGTGTATTTACTTCTGATCTGATCTTCAAGTGAAACTATGATGCTCTGAAAATTCTAATCTTGA
* *
2873247 TCCTCTTGCTCCTCTGAACCTACGTGTAAAAATACTTACACGCTAAGTCATAGACTTAGTGAGGC
196 TCCTCTTGCTCCTCTGAACCTACGTGTAAAAACACTTACACGCTAAGTCATAGACTTAGTGAAGC
2873312 AC
261 AC
2873314 AAAACTATCA
Statistics
Matches: 246, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
264 246 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (264 bp):
TAAACTTTAAACTTTTATTAACAAAAAAGTCATACATACATAATTGAGTTCGAAACATTACAAAA
TTCATCAGAGCATACATAAATAACACCTTTGTACATGCCAACTATTTGACTCAACAAAATACCTA
CTGTGTATTTACTTCTGATCTGATCTTCAAGTGAAACTATGATGCTCTGAAAATTCTAATCTTGA
TCCTCTTGCTCCTCTGAACCTACGTGTAAAAACACTTACACGCTAAGTCATAGACTTAGTGAAGC
ACTT
Found at i:2873616 original size:22 final size:22
Alignment explanation
Indices: 2873576--2873626 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2873566 CTAAGTGGCA
*
2873576 TATGAAATATATCCCGAAGGACC
1 TATG-AATATATCCCGAAGAACC
* *
2873599 TATGAATATGTCCTGAAGAACC
1 TATGAATATATCCCGAAGAACC
2873621 TATGAA
1 TATGAA
2873627 ACCCTCGACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (22 bp):
TATGAATATATCCCGAAGAACC
Found at i:2878386 original size:22 final size:21
Alignment explanation
Indices: 2878360--2878426 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
2878350 TGGCATGTGA
*
2878360 AATATATCCCGAATGACCTATG
1 AATATGTCCCGAA-GACCTATG
* *
2878382 AATATGTCCTGAAGAACCAATG
1 AATATGTCCCGAAG-ACCTATG
*
2878404 AATATGTCCCAAAGGACCTATG
1 AATATGTCCCGAA-GACCTATG
2878426 A
1 A
2878427 TACCTTCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (21 bp):
AATATGTCCCGAAGACCTATG
Found at i:2882992 original size:22 final size:22
Alignment explanation
Indices: 2882966--2883011 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2882956 TGGCATGTGA
2882966 AATATGTCTCGAAGGACCTATG
1 AATATGTCTCGAAGGACCTATG
2882988 AATATGTCTCGAAGGACCTATG
1 AATATGTCTCGAAGGACCTATG
2883010 AA
1 AA
2883012 ACCCTCGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (22 bp):
AATATGTCTCGAAGGACCTATG
Found at i:2890520 original size:55 final size:55
Alignment explanation
Indices: 2890440--2890816 Score: 547
Period size: 55 Copynumber: 6.9 Consensus size: 55
2890430 TGACACTATA
* ** * *
2890440 TGTGTGCAAAACTAAGAAATTCATAATAGGTTTATGAATTTTTGTATGGGTACTA
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * * * * * *
2890495 TGTTTACAAAACTAAGAAACTCATAATATGTTTATGAATTTCTGTATAGGCATTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2890550 TGTGTCCAAAACTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2890605 TGTGTGCAAAAGTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2890660 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTA
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * *
2890715 TGTGTACAAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
2890770 TGTGTGCAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTAT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
2890817 TGGTATTAGG
Statistics
Matches: 287, Mismatches: 35, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 287 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (55 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
Found at i:2890863 original size:110 final size:110
Alignment explanation
Indices: 2890440--2890907 Score: 383
Period size: 110 Copynumber: 4.3 Consensus size: 110
2890430 TGACACTATA
* ** * * * *
2890440 TGTGTGCAAAACTAAGAAATTCATAAT-AGGTTTATGAATTTTTGTATGGGTACTATGTTTACAA
1 TGTGTGCAAAACTAAGAAATTTATAATGA-GTTTATGAATTTCCGTATTGGCACTAGGTATACAA
* * * * * * * *
2890504 AACTAAGAAACTCATAATATGTTTATGAA-TTTCTGTATAGGCATTG
65 AACCAAGAAATTCATAACAAGGTGATGAATTTTC-GTATGGGCACTG
* * * * * * *
2890550 TGTGTCCAAAACTAAGAAATTCATAATAAATTTATGAATTTCCGTATGGGCACT-GTGTGTGCAA
1 TGTGTGCAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTATTGGCACTAG-GTATACAA
** * * *
2890614 AAGTAAGAAATTCATAATAAGTTTATGAA-TTTCTGTATGGGCACTG
65 AACCAAGAAATTCATAACAAGGTGATGAATTTTC-GTATGGGCACTG
* * * *
2890660 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTACAAA
1 TGTGTGCAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTATTGGCACTAGGTATACAAA
** * * *
2890725 ATTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
66 ACCAAGAAATTCATAACAAGGTGATGAATTTTCGTATGGGCACTG
* * * **
2890770 TGTGTGCAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTATTGGTATTAGGTATGCATC
1 TGTGTGCAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTATTGGCACTAGGTATACAAA
* * * * * * *
2890835 CCCACGAAATTCTTAACGAGGTGGTGAATTATT-GTATTGGCACTA
66 ACCAAGAAATTCATAACAAGGTGATGAATT-TTCGTATGGGCACTG
* *
2890880 CGAGTGC-AAACTAA-AGAATTTATAATGA
1 TGTGTGCAAAACTAAGA-AATTTATAATGA
2890908 AATTAAATAG
Statistics
Matches: 310, Mismatches: 42, Indels: 13
0.85 0.12 0.04
Matches are distributed among these distances:
108 1 0.00
109 19 0.06
110 283 0.91
111 7 0.02
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (110 bp):
TGTGTGCAAAACTAAGAAATTTATAATGAGTTTATGAATTTCCGTATTGGCACTAGGTATACAAA
ACCAAGAAATTCATAACAAGGTGATGAATTTTCGTATGGGCACTG
Found at i:2891055 original size:49 final size:49
Alignment explanation
Indices: 2890975--2891086 Score: 154
Period size: 49 Copynumber: 2.3 Consensus size: 49
2890965 AAAAGACTAA
* * *
2890975 ATGCCTAACTGTGC-TTTTTGGCATAAAGGTGCCATTAATGCAAGTTAG
1 ATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* *
2891023 ATGCCTAACGGTGCATTTTTGGTAGAATGGTGCCACTAATGCAAGTTAG
1 ATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
**
2891072 ATGAATAACGGTGCA
1 ATGCCTAACGGTGCA
2891087 ATACTGGCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
48 13 0.23
49 43 0.77
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (49 bp):
ATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
Found at i:2894053 original size:18 final size:18
Alignment explanation
Indices: 2894027--2894062 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2894017 GCTAAAATGT
*
2894027 TCAGAGGTATCGATACCC
1 TCAGAGGTATCCATACCC
*
2894045 TCAGGGGTATCCATACCC
1 TCAGAGGTATCCATACCC
2894063 CCATGAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (18 bp):
TCAGAGGTATCCATACCC
Found at i:2895537 original size:14 final size:15
Alignment explanation
Indices: 2895512--2895545 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2895502 GATGTTGAAG
*
2895512 GAAGAGGAAGAAAAT
1 GAAGAGGAAGAAAAA
2895527 GAAGA-GAAGAAAAA
1 GAAGAGGAAGAAAAA
2895541 GAAGA
1 GAAGA
2895546 AGGAGGTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (15 bp):
GAAGAGGAAGAAAAA
Found at i:2900396 original size:18 final size:18
Alignment explanation
Indices: 2900366--2900409 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2900356 GACAAAAGTG
*
2900366 CAGACTACCAGTCCTTTT
1 CAGACTGCCAGTCCTTTT
*
2900384 CATACTGCCAGTCCTTTT
1 CAGACTGCCAGTCCTTTT
2900402 CAGACTGC
1 CAGACTGC
2900410 ATTTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (18 bp):
CAGACTGCCAGTCCTTTT
Found at i:2903199 original size:26 final size:26
Alignment explanation
Indices: 2903163--2903215 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2903153 GGATCCGATG
*
2903163 CGAGTGGAAGAATTTAATTTTCGAGC
1 CGAGTAGAAGAATTTAATTTTCGAGC
2903189 CGAGTAGAAGAATTTAATTTTCGAGC
1 CGAGTAGAAGAATTTAATTTTCGAGC
2903215 C
1 C
2903216 AAGTCCGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (26 bp):
CGAGTAGAAGAATTTAATTTTCGAGC
Found at i:2909717 original size:78 final size:77
Alignment explanation
Indices: 2909579--2910017 Score: 297
Period size: 78 Copynumber: 5.7 Consensus size: 77
2909569 ATTAATTCCA
* * * *
2909579 AAGACCAAGAGGGTAAAGAAACTTGTTTGAACATTGATGTTGGCCACCAAGATAATAATAAGCCT
1 AAGATCAAAAGGGTAAAGAAACTAGTTTGAACACTGATGTTGGCCACCAAGATAATAATAAGCCT
* * *
2909644 CCGCTCAAGAGAG
66 ACAC-CAACAGAG
* * *
2909657 AAGATCAAAAGGGTAAAGAAACTAGTTTGAACACTGATGTTGAG-CACTAGGATACTAATAAGCC
1 AAGATCAAAAGGGTAAAGAAACTAGTTTGAACACTGATGTTG-GCCACCAAGATAATAATAAGCC
*
2909721 TACACCAACATAG
65 TACACCAACAGAG
* * ** ** * * *
2909734 AAGATCATAAA-GGTAAAGGAGCT-GATTTGGGCTTTGTTGTTGGCCA--AAGATGCA-AATAAC
1 AAGATCA-AAAGGGTAAAGAAACTAG-TTTGAACACTGATGTTGGCCACCAAGAT-AATAATAAG
* * *
2909794 CCTAAACCAA-ATAT
63 CCTACACCAACAGAG
* * * * * *
2909808 ATAGGATCAAGAA-GGTAAAGAAACTGGTTCGAACATTGATGTTGGCTACCAGGATACTAATAAG
1 A-A-GATCAA-AAGGGTAAAGAAACTAGTTTGAACACTGATGTTGGCCACCAAGATAATAATAAG
2909872 CCTACACCCAAC-GTAG
63 CCTACA-CCAACAG-AG
* * * * * * *
2909888 AAGATCATAATGGTAAAGAAACTTGTTCGAACA-TCGATTTTGGCCACCAGGATACTAATAAGCC
1 AAGATCAAAAGGGTAAAGAAACTAGTTTGAACACT-GATGTTGGCCACCAAGATAATAATAAGCC
*
2909952 TACACCCAACATAG
65 TACA-CCAACAGAG
* * * * * *
2909966 GAGATCATAAGAGTAAAGAAA-TTGTTTTGACCATTGATGTTGGCCACCAAGA
1 AAGATCAAAAGGGTAAAGAAACTAG-TTTGAACACTGATGTTGGCCACCAAGA
2910018 AACTGGTTTG
Statistics
Matches: 290, Mismatches: 51, Indels: 40
0.76 0.13 0.10
Matches are distributed among these distances:
74 4 0.01
75 20 0.07
76 34 0.12
77 44 0.15
78 179 0.62
79 7 0.02
80 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (77 bp):
AAGATCAAAAGGGTAAAGAAACTAGTTTGAACACTGATGTTGGCCACCAAGATAATAATAAGCCT
ACACCAACAGAG
Found at i:2910028 original size:33 final size:33
Alignment explanation
Indices: 2909981--2910047 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2909971 CATAAGAGTA
* * *
2909981 AAGAAATTGTTTTGACCATTGATGTTGGCCACC
1 AAGAAACTGGTTTGAACATTGATGTTGGCCACC
2910014 AAGAAACTGGTTTGAACATTGATGTTGGCCACC
1 AAGAAACTGGTTTGAACATTGATGTTGGCCACC
2910047 A
1 A
2910048 GGATACTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (33 bp):
AAGAAACTGGTTTGAACATTGATGTTGGCCACC
Found at i:2911595 original size:2 final size:2
Alignment explanation
Indices: 2911588--2911626 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2911578 ATTTTGACTT
2911588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2911627 GAATCCCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2912896 original size:32 final size:32
Alignment explanation
Indices: 2912737--2912898 Score: 117
Period size: 32 Copynumber: 5.1 Consensus size: 32
2912727 ATGCTCTGTA
* * * *
2912737 CATTAACTGAATGCAACACTAACTCTGCTGTG
1 CATTATCTAAATGCAACACTAACTCTACTATG
* * * *
2912769 CATTATCTAAGTTCAACACTGATTCTACTATG
1 CATTATCTAAATGCAACACTAACTCTACTATG
* * * * * * *
2912801 CATTATCTTAATGTAATACTGATTATACTGTG
1 CATTATCTAAATGCAACACTAACTCTACTATG
* * * * * *
2912833 TATTATTTGAATGCAATACTTACTCTTCTATG
1 CATTATCTAAATGCAACACTAACTCTACTATG
* *
2912865 AATTATCTAAATGCAACACTAACACTACTATG
1 CATTATCTAAATGCAACACTAACTCTACTATG
2912897 CA
1 CA
2912899 ACACACAAGC
Statistics
Matches: 98, Mismatches: 32, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.36
Consensus pattern (32 bp):
CATTATCTAAATGCAACACTAACTCTACTATG
Found at i:2913888 original size:21 final size:20
Alignment explanation
Indices: 2913850--2913889 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2913840 TTTACACCAA
**
2913850 TTCATCCAATATTGATATTG
1 TTCATCCAATATCAATATTG
2913870 TTCATCCCAATATCAATATT
1 TTCAT-CCAATATCAATATT
2913890 TGAACCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (20 bp):
TTCATCCAATATCAATATTG
Found at i:2933969 original size:23 final size:23
Alignment explanation
Indices: 2933939--2933987 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2933929 GGTGGTTTGG
*
2933939 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
2933962 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
2933985 TTT
1 TTT
2933988 GGTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:2936267 original size:21 final size:21
Alignment explanation
Indices: 2936243--2936286 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2936233 TCTACTTCAA
*
2936243 TTAAGAATCAAGGAGCTTTAC
1 TTAAGAATCAAGGAGCCTTAC
* * *
2936264 TTAATAGTCAAGGCGCCTTAC
1 TTAAGAATCAAGGAGCCTTAC
2936285 TT
1 TT
2936287 CAAAGCCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (21 bp):
TTAAGAATCAAGGAGCCTTAC
Found at i:2940831 original size:20 final size:20
Alignment explanation
Indices: 2940808--2940852 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2940798 TTAACTTTTT
*
2940808 CTTTTCTCTTTC-TTCCTTAA
1 CTTTTCTATTTCATT-CTTAA
*
2940828 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATTCTTAA
2940848 CTTTT
1 CTTTT
2940853 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTATTTCATTCTTAA
Found at i:2945161 original size:248 final size:252
Alignment explanation
Indices: 2944717--2945218 Score: 949
Period size: 248 Copynumber: 2.0 Consensus size: 252
2944707 ATTTTCAACA
*
2944717 CTAAACATCTTATCTTGCCACTGTATTTCCATCTACTACACCATCAGATCATTCATTTGCATCCA
1 CTAAACATCTTATCTTGCCACTGCATTTCCATCTACTA-ACCATCAGATCATTCATTTGCATCCA
2944782 TCAGCATACACATTTTCATTTTTCGTGACATGTGTATATATAAAGACTAACTATACATAGATAGA
65 TCAGCATACACATTTTCATTTTTCGTGACATGTG-ATATATAAAGACTAACTATACATAGATAGA
2944847 TTAATACTTAGCTTTGTTTATACTTTTGTAATTTCGCCCAATCCTTGTGGAGACGATACTCACTC
129 TTAATACTTAGCTTTGTTTATACTTTTGTAATTTCGCCCAATCCTTGTGGAGACGATACTCACTC
2944912 ATCATTATATTACTTGAACGATTGTGTATACTTGCACATTATCTGCATATATTTTATAG
194 ATCATTATATTACTTGAACGATTGTGTATACTTGCACATTATCTGCATATATTTTATAG
2944971 CTAAACATCTTATCTTGCCACTGCATTTCCATCTACT-ACCATCAGATCATTCATTTGCATCCAT
1 CTAAACATCTTATCTTGCCACTGCATTTCCATCTACTAACCATCAGATCATTCATTTGCATCCAT
2945035 CAGCATACACATTTTCA-TTTTCGTGACATGTG-TATATAAAGACTAACTATACATAGATAGATT
66 CAGCATACACATTTTCATTTTTCGTGACATGTGATATATAAAGACTAACTATACATAGATAGATT
2945098 AATACTTAGC-TTGTTTATACTTTTGTAATTTCGCCCAATCCTTGTGGAGACGATACTCACTCAT
131 AATACTTAGCTTTGTTTATACTTTTGTAATTTCGCCCAATCCTTGTGGAGACGATACTCACTCAT
2945162 CATTATATTACTTGAACGATTGTGTATACTTGCACATTATCTGCATATATTTTATAG
196 CATTATATTACTTGAACGATTGTGTATACTTGCACATTATCTGCATATATTTTATAG
2945219 TACTCACACA
Statistics
Matches: 247, Mismatches: 1, Indels: 6
0.97 0.00 0.02
Matches are distributed among these distances:
248 111 0.45
249 41 0.17
251 15 0.06
252 44 0.18
254 36 0.15
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (252 bp):
CTAAACATCTTATCTTGCCACTGCATTTCCATCTACTAACCATCAGATCATTCATTTGCATCCAT
CAGCATACACATTTTCATTTTTCGTGACATGTGATATATAAAGACTAACTATACATAGATAGATT
AATACTTAGCTTTGTTTATACTTTTGTAATTTCGCCCAATCCTTGTGGAGACGATACTCACTCAT
CATTATATTACTTGAACGATTGTGTATACTTGCACATTATCTGCATATATTTTATAG
Found at i:2946044 original size:20 final size:20
Alignment explanation
Indices: 2946000--2946090 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
2945990 CAATCAAAAG
* **
2946000 TATCGATATTATTCATGTTGA
1 TATCGATATCATTCAT-CAGA
* *
2946021 TATCAACATCATTCATCAGA
1 TATCGATATCATTCATCAGA
2946041 TATCGATATCATTCATCAGA
1 TATCGATATCATTCATCAGA
2946061 TATCGATATCATTCAT-AGA
1 TATCGATATCATTCATCAGA
2946080 TATCGATATCA
1 TATCGATATCA
2946091 AGGGTTTAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
19 14 0.22
20 36 0.57
21 13 0.21
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (20 bp):
TATCGATATCATTCATCAGA
Found at i:2947531 original size:3 final size:3
Alignment explanation
Indices: 2947523--2947550 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2947513 TATATCATGC
2947523 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2947551 ATTTTGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2950528 original size:20 final size:20
Alignment explanation
Indices: 2950503--2950548 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2950493 CTGATGTTAC
*
2950503 CGATACTAACCCTTCAATAT
1 CGATACTAACCCCTCAATAT
* *
2950523 CGATACTAACCCCTGAGTAT
1 CGATACTAACCCCTCAATAT
2950543 CGATAC
1 CGATAC
2950549 CCACATCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (20 bp):
CGATACTAACCCCTCAATAT
Found at i:2960046 original size:75 final size:74
Alignment explanation
Indices: 2959959--2960114 Score: 296
Period size: 75 Copynumber: 2.1 Consensus size: 74
2959949 GCATGGTTTT
2959959 AAAA-AATTGAAAGTTTAGGTACTAAAACAGAACAAAATTGATAATTTAGGTACTAAACACATAA
1 AAAATAATTGAAAGTTTAGGTACTAAAACAGAACAAAATTGATAATTTAGGTACTAAACACATAA
2960023 TTTACTCAA
66 TTTACTCAA
2960032 AATAATAATTGAAAGTTTAGGTACTAAAACAGAACAAAATTGATAATTTAGGTACTAAACACATA
1 AA-AATAATTGAAAGTTTAGGTACTAAAACAGAACAAAATTGATAATTTAGGTACTAAACACATA
2960097 ATTTACTCAA
65 ATTTACTCAA
2960107 AAAATAAT
1 AAAATAAT
2960115 GAGGCCCATG
Statistics
Matches: 81, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
73 2 0.02
74 8 0.10
75 71 0.88
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (74 bp):
AAAATAATTGAAAGTTTAGGTACTAAAACAGAACAAAATTGATAATTTAGGTACTAAACACATAA
TTTACTCAA
Found at i:2965273 original size:220 final size:220
Alignment explanation
Indices: 2964878--2965317 Score: 839
Period size: 220 Copynumber: 2.0 Consensus size: 220
2964868 AACTATTCCG
2964878 AGATAAAGAAAGTGAGATTGGTAGCCATGGAGTTCATATACTATGCTTTAATATGGTGGGATCAA
1 AGATAAAGAAAGTGAGATTGGTAGCCATGGAGTTCATATACTATGCTTTAATATGGTGGGATCAA
*
2964943 CTTACCCTTAACAGAAGGAGGAATGGAGAAAGATCGGTCTTAACTTGGCATGGAATGAAAGGTAT
66 CTTACCCTTAACAGAAGGAGGAATGGAGAAAGATCGGTCTTAACTTGGCATGAAATGAAAGGTAT
2965008 AATGCGGAAACGATTCATTCCTGTTCATTATCACCGACACTTGTTTCAAAAATTATAGAATCTCA
131 AATGCGGAAACGATTCATTCCTGTTCATTATCACCGACACTTGTTTCAAAAATTATAGAATCTCA
2965073 A-CGAAGGCCAAAGGAGTGTGGAGGA
196 AGC-AAGGCCAAAGGAGTGTGGAGGA
2965098 AGAT-AAGAAAGTGGAGATTGGTAGCCATGGAGTTCATATACTATGCTTTAATATGGTGGGATCA
1 AGATAAAGAAAGT-GAGATTGGTAGCCATGGAGTTCATATACTATGCTTTAATATGGTGGGATCA
2965162 ACTTACCCTTAACAGAAGGAGGAATGGAGAAAGATCGGTCTTAACTTGGCATGAAATGAAAGGTA
65 ACTTACCCTTAACAGAAGGAGGAATGGAGAAAGATCGGTCTTAACTTGGCATGAAATGAAAGGTA
2965227 TAATGCGGAAACGATTCATTCCTGTTCATTATCACCGACACTTGTTTCAAAAATTATAGAATCTC
130 TAATGCGGAAACGATTCATTCCTGTTCATTATCACCGACACTTGTTTCAAAAATTATAGAATCTC
2965292 AAGCAAGGCCAAAGGAGTGTGGAGGA
195 AAGCAAGGCCAAAGGAGTGTGGAGGA
2965318 CTATTATAAA
Statistics
Matches: 217, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
219 8 0.04
220 208 0.96
221 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (220 bp):
AGATAAAGAAAGTGAGATTGGTAGCCATGGAGTTCATATACTATGCTTTAATATGGTGGGATCAA
CTTACCCTTAACAGAAGGAGGAATGGAGAAAGATCGGTCTTAACTTGGCATGAAATGAAAGGTAT
AATGCGGAAACGATTCATTCCTGTTCATTATCACCGACACTTGTTTCAAAAATTATAGAATCTCA
AGCAAGGCCAAAGGAGTGTGGAGGA
Found at i:2966887 original size:37 final size:37
Alignment explanation
Indices: 2966837--2966911 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2966827 TGTGATCCAA
2966837 ATTAGCAACATGAATGTCCTTGCATCTCCAACCTTTC
1 ATTAGCAACATGAATGTCCTTGCATCTCCAACCTTTC
2966874 ATTAGCAACATGAATGTCCTTGCATCTCCAACCTTTC
1 ATTAGCAACATGAATGTCCTTGCATCTCCAACCTTTC
2966911 A
1 A
2966912 CAATAATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (37 bp):
ATTAGCAACATGAATGTCCTTGCATCTCCAACCTTTC
Found at i:2973256 original size:23 final size:23
Alignment explanation
Indices: 2973226--2973338 Score: 145
Period size: 23 Copynumber: 4.9 Consensus size: 23
2973216 TGCCACATAT
*
2973226 TTGTCCTGAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
*
2973249 TTGTCCTGAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATAGGA
**
2973272 TTGTCCCGAAGGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGGA
* **
2973295 TTGTCCCGAATGACCACATAGTT
1 TTGTCCCGAAGGACCACATAGGA
* *
2973318 TTGTCGCAAAGGACCACATAG
1 TTGTCCCGAAGGACCACATAG
2973339 AACCCTCGAC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGA
Found at i:2973311 original size:69 final size:67
Alignment explanation
Indices: 2973210--2973338 Score: 163
Period size: 69 Copynumber: 1.9 Consensus size: 67
2973200 ATAAATTGCA
* *
2973210 CCGAAGTGCCACATATTTGTCCTGAAGGACCACATAGGATTGTC-CTGAAGGACCACATAGGATT
1 CCGAAGTGCCACATATTTGTCCCGAAGGACCACATAGGATTGTCGC-AAAGGACCACATAGGATT
2973274 GTC
65 GTC
* **
2973277 CCGAAG-GACCACATAGTTTTGTCCCGAATGACCACATAGTTTTGTCGCAAAGGACCACATAG
1 CCGAAGTG-CCACATA--TTTGTCCCGAAGGACCACATAGGATTGTCGCAAAGGACCACATAG
2973339 AACCCTCGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
66 1 0.02
67 13 0.25
69 38 0.72
70 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (67 bp):
CCGAAGTGCCACATATTTGTCCCGAAGGACCACATAGGATTGTCGCAAAGGACCACATAGGATTG
TC
Found at i:2973475 original size:15 final size:14
Alignment explanation
Indices: 2973446--2973497 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
2973436 GTGTGTCTTG
2973446 TTCACATAGGCATT
1 TTCACATAGGCATT
*
2973460 TTCACATCGAGCATT
1 TTCACATAG-GCATT
* * *
2973475 TTCATATAAAGCATA
1 TTCACAT-AGGCATT
2973490 TTCACATA
1 TTCACATA
2973498 TCACATTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (14 bp):
TTCACATAGGCATT
Found at i:2976380 original size:23 final size:22
Alignment explanation
Indices: 2976354--2976413 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
2976344 ATATAAAATT
* **
2976354 TGTCATGAAAGACCGTATAGAAA
1 TGTCCTGAAAGACCACATAG-AA
*
2976377 TGTCCTGAAATACCACATAGAA
1 TGTCCTGAAAGACCACATAGAA
2976399 -GTCCTGAAAGACCAC
1 TGTCCTGAAAGACCAC
2976414 TCTTTAAGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 14 0.44
22 2 0.06
23 16 0.50
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (22 bp):
TGTCCTGAAAGACCACATAGAA
Found at i:2976704 original size:14 final size:15
Alignment explanation
Indices: 2976675--2976708 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2976665 CGTAGAGTCT
*
2976675 CATATCTCATTATCA
1 CATATATCATTATCA
2976690 CATATATCA-TATCA
1 CATATATCATTATCA
2976704 CATAT
1 CATAT
2976709 TCTTGTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (15 bp):
CATATATCATTATCA
Found at i:2980432 original size:2 final size:2
Alignment explanation
Indices: 2980390--2980416 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2980380 TACTTATCAT
2980390 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2980417 CATAAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2980620 original size:21 final size:21
Alignment explanation
Indices: 2980594--2980651 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
2980584 ATATAAAATT
* *
2980594 TATCCCGAAGGACCACATATA
1 TATCCCGAAAGACCACATAAA
*
2980615 TATCCCGAAAGACCAGATAAA
1 TATCCCGAAAGACCACATAAA
*
2980636 TATCCCGAATGACCAC
1 TATCCCGAAAGACCAC
2980652 TCCTTAAGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (21 bp):
TATCCCGAAAGACCACATAAA
Found at i:2980724 original size:42 final size:42
Alignment explanation
Indices: 2980665--2980747 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
2980655 TTAAGGATCA
* *
2980665 CATATACATTCCAAAGGACCAAATATGTGTCCCGAAGAACCG
1 CATATACATTCCAAAGGACCAAATATATATCCCGAAGAACCG
* ** *
2980707 CATATATATTCCAAAGGATTACATATATATCCCGAAGAACC
1 CATATACATTCCAAAGGACCAAATATATATCCCGAAGAACC
2980748 ACGTAGAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (42 bp):
CATATACATTCCAAAGGACCAAATATATATCCCGAAGAACCG
Found at i:2986571 original size:23 final size:22
Alignment explanation
Indices: 2986492--2986572 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
2986482 TAAATTACAT
*
2986492 CGAAGTACCACATA-TTTGTCC
1 CGAAGGACCACATAGTTTGTCC
* * * * *
2986513 TGAAGAACCACAAAGGATTATCC
1 CGAAGGACCACATA-GTTTGTCC
2986536 CGAAGGACCACATAGTTTTGTCC
1 CGAAGGACCACATAG-TTTGTCC
*
2986559 GGAAGGACCACATA
1 CGAAGGACCACATA
2986573 AAACCCTCGA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 11 0.24
22 1 0.02
23 34 0.74
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.21
Consensus pattern (22 bp):
CGAAGGACCACATAGTTTGTCC
Found at i:2986700 original size:14 final size:15
Alignment explanation
Indices: 2986681--2986713 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2986671 GTGTGTCTTG
2986681 TTCACATAG-GCATT
1 TTCACATAGAGCATT
*
2986695 TTCACATCGAGCATT
1 TTCACATAGAGCATT
2986710 TTCA
1 TTCA
2986714 TATAAGCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.36
Consensus pattern (15 bp):
TTCACATAGAGCATT
Found at i:3000065 original size:23 final size:23
Alignment explanation
Indices: 3000031--3000086 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3000021 AGTAAGATTC
* *
3000031 CCATGAAGCTCATGGTTCCAGGA
1 CCATGAATCTCATGGTTCCAAGA
*
3000054 TCATGAATCTCATGGTTCCAAGA
1 CCATGAATCTCATGGTTCCAAGA
3000077 CCATGAATCT
1 CCATGAATCT
3000087 TAACTTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (23 bp):
CCATGAATCTCATGGTTCCAAGA
Found at i:3005491 original size:23 final size:24
Alignment explanation
Indices: 3005445--3005492 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3005435 TGGGCCGAAA
3005445 TCGGATTTAAAATGACTTCCTAAT
1 TCGGATTTAAAATGACTTCCTAAT
3005469 TCGGATTTAAAATGA-TTCCTAAT
1 TCGGATTTAAAATGACTTCCTAAT
3005492 T
1 T
3005493 GACAATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (24 bp):
TCGGATTTAAAATGACTTCCTAAT
Found at i:3013523 original size:22 final size:21
Alignment explanation
Indices: 3013487--3013527 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3013477 CATCTCCATT
3013487 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
3013508 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
3013528 TTTTGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:3013848 original size:18 final size:18
Alignment explanation
Indices: 3013825--3013859 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3013815 AAATTGGAGT
3013825 ACAAAAAGAA-AAGAAAAG
1 ACAAAAA-AATAAGAAAAG
3013843 ACAAAAAAATAAGAAAA
1 ACAAAAAAATAAGAAAA
3013860 ATTTCAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (18 bp):
ACAAAAAAATAAGAAAAG
Found at i:3019100 original size:22 final size:21
Alignment explanation
Indices: 3019064--3019104 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3019054 CATCTCCATT
3019064 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
3019085 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
3019105 TTTCGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:3020682 original size:20 final size:20
Alignment explanation
Indices: 3020657--3020706 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3020647 AAGTGAGTAG
*
3020657 TATCAATACTCTACTCGTAT
1 TATCAATACTCTACTCGTAC
* *
3020677 TATCAATACTGTACTTGTAC
1 TATCAATACTCTACTCGTAC
*
3020697 TATCGATACT
1 TATCAATACT
3020707 ACCGGAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (20 bp):
TATCAATACTCTACTCGTAC
Found at i:3024161 original size:20 final size:20
Alignment explanation
Indices: 3024136--3024184 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3024126 TCAACTCTTC
3024136 ATCATATTCTCAAAACTATG
1 ATCATATTCTCAAAACTATG
3024156 ATCATATTCTCAAAACTATG
1 ATCATATTCTCAAAACTATG
*
3024176 ATCCTATTC
1 ATCATATTC
3024185 CTGACTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (20 bp):
ATCATATTCTCAAAACTATG
Found at i:3025194 original size:18 final size:18
Alignment explanation
Indices: 3025179--3025217 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3025169 GATTACATGC
3025179 CAACATTTATTTACATAA
1 CAACATTTATTTACATAA
3025197 CAACATTTATTTACATAA
1 CAACATTTATTTACATAA
3025215 CAA
1 CAA
3025218 AATGACCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (18 bp):
CAACATTTATTTACATAA
Found at i:3025611 original size:23 final size:23
Alignment explanation
Indices: 3025593--3025653 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3025583 CTCGTATAAA
3025593 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
3025616 TGTACCAAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
3025639 TGCATCGTAGTGCCA
1 TGCACCGAAGTGCCA
3025654 TATAAGATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3026366 original size:65 final size:65
Alignment explanation
Indices: 3026293--3026416 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 65
3026283 ATCCCTTGAC
3026293 GGGTGCATCGATGCACTATCTAT-T-CATCGATACA-TAAAT-CCTATTCGATGTTTGTATTTAA
1 GGGTGCATCGATGCACTA-CT-TGTGCATCGATACACT-AATGCC-ATTCGATGTTTGTATTTAA
3026354 GGGG
62 GGGG
* *
3026358 GGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTGTATTT
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGCCATTCGATGTTTGTATTT
3026417 TACACCTTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
63 1 0.02
64 3 0.06
65 47 0.89
66 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (65 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGCCATTCGATGTTTGTATTTAAGGGG
Found at i:3028885 original size:23 final size:23
Alignment explanation
Indices: 3028855--3028932 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
3028845 GGCTTGGATG
3028855 AATAAAACCCTTTTTTCTTGTAA
1 AATAAAACCCTTTTTTCTTGTAA
**** * *
3028878 AATAAAACCC--AAAGCTTGGATG
1 AATAAAACCCTTTTTTCTTGTA-A
3028900 AATAAAACCCTTTTTTCTTGTAA
1 AATAAAACCCTTTTTTCTTGTAA
3028923 AATAAAACCC
1 AATAAAACCC
3028933 AAAGCTTGGA
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
21 5 0.12
22 10 0.25
23 20 0.50
24 5 0.12
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (23 bp):
AATAAAACCCTTTTTTCTTGTAA
Found at i:3028910 original size:45 final size:45
Alignment explanation
Indices: 3028846--3028943 Score: 196
Period size: 45 Copynumber: 2.2 Consensus size: 45
3028836 CCTCCTTAAG
3028846 GCTTGGATGAATAAAACCCTTTTTTCTTGTAAAATAAAACCCAAA
1 GCTTGGATGAATAAAACCCTTTTTTCTTGTAAAATAAAACCCAAA
3028891 GCTTGGATGAATAAAACCCTTTTTTCTTGTAAAATAAAACCCAAA
1 GCTTGGATGAATAAAACCCTTTTTTCTTGTAAAATAAAACCCAAA
3028936 GCTTGGAT
1 GCTTGGAT
3028944 ATTAAAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (45 bp):
GCTTGGATGAATAAAACCCTTTTTTCTTGTAAAATAAAACCCAAA
Found at i:3036847 original size:7 final size:7
Alignment explanation
Indices: 3036835--3036862 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3036825 GGGTTCGGTC
3036835 GGTTAAT
1 GGTTAAT
3036842 GGTTAAT
1 GGTTAAT
3036849 GGTTAAT
1 GGTTAAT
3036856 GGTTAAT
1 GGTTAAT
3036863 AGTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
GGTTAAT
Found at i:3037523 original size:23 final size:23
Alignment explanation
Indices: 3037497--3037553 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
3037487 TTCGTTTAGC
*
3037497 GTTCGTGAACATATTTA-TTTAAT
1 GTTCGTGAACATATTTACTAT-AT
3037520 GTTCGT-AGACATATTTACTATAT
1 GTTCGTGA-ACATATTTACTATAT
3037543 GTTCGTGAACA
1 GTTCGTGAACA
3037554 CGTTCATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.03
23 26 0.87
24 3 0.10
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (23 bp):
GTTCGTGAACATATTTACTATAT
Found at i:3041196 original size:14 final size:14
Alignment explanation
Indices: 3041177--3041209 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3041167 TGGGGAGTAA
*
3041177 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
3041191 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
3041205 TCCCT
1 TCCCT
3041210 ATATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:3044244 original size:19 final size:18
Alignment explanation
Indices: 3044220--3044269 Score: 77
Period size: 16 Copynumber: 2.8 Consensus size: 18
3044210 AATGCAATTA
3044220 GTGTACCGATACACCTATG
1 GTGTACCGATACACCT-TG
3044239 GTGTACCGATACA--TTG
1 GTGTACCGATACACCTTG
3044255 GTGTACCGATACACC
1 GTGTACCGATACACC
3044270 CTGCAGTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 15 0.52
17 1 0.03
19 13 0.45
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (18 bp):
GTGTACCGATACACCTTG
Found at i:3044347 original size:21 final size:21
Alignment explanation
Indices: 3044321--3044424 Score: 172
Period size: 21 Copynumber: 5.0 Consensus size: 21
3044311 TTTGAATTTA
* * *
3044321 ATGAAGGAGTATCGATACCTT
1 ATGAAGGGGTACCGATACCCT
3044342 ATGAAGGGGTACCGATACCCT
1 ATGAAGGGGTACCGATACCCT
3044363 ATGAAGGGGTACCGATACCCT
1 ATGAAGGGGTACCGATACCCT
3044384 ATGAAGGGGTACCGATACCCT
1 ATGAAGGGGTACCGATACCCT
*
3044405 ATGAAGGGGTACTGATACCC
1 ATGAAGGGGTACCGATACCC
3044425 CTATTATTGG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (21 bp):
ATGAAGGGGTACCGATACCCT
Found at i:3044609 original size:20 final size:20
Alignment explanation
Indices: 3044584--3044630 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3044574 GTCTGGCAAT
3044584 GAACCGGCTGAAAACCGATA
1 GAACCGGCTGAAAACCGATA
* *
3044604 GAACCGACTGAAAACCGGTA
1 GAACCGGCTGAAAACCGATA
*
3044624 AAACCGG
1 GAACCGG
3044631 GGTGAACCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.26, T:0.09
Consensus pattern (20 bp):
GAACCGGCTGAAAACCGATA
Found at i:3044645 original size:30 final size:30
Alignment explanation
Indices: 3044604--3044669 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3044594 AAAACCGATA
3044604 GAACCGACTGAAAACCGGTAAAACCGGGGT
1 GAACCGACTGAAAACCGGTAAAACCGGGGT
* * **
3044634 GAACCGGCTGAAAACTGGTAAAACCGGTTT
1 GAACCGACTGAAAACCGGTAAAACCGGGGT
3044664 GAACCG
1 GAACCG
3044670 CCGATTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.23, G:0.29, T:0.14
Consensus pattern (30 bp):
GAACCGACTGAAAACCGGTAAAACCGGGGT
Found at i:3048404 original size:21 final size:18
Alignment explanation
Indices: 3048357--3048394 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3048347 CAACAATTGG
3048357 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
*
3048375 TAACAATTGATATCCTTT
1 TAACAATTGATATCTTTT
3048393 TA
1 TA
3048395 TTGACAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:3049160 original size:2 final size:2
Alignment explanation
Indices: 3049147--3049184 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3049137 CCTTATTATT
*
3049147 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3049185 TTTATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3049189 original size:7 final size:7
Alignment explanation
Indices: 3049139--3049205 Score: 52
Period size: 8 Copynumber: 9.7 Consensus size: 7
3049129 AATTTAACCC
3049139 TTAT-TA
1 TTATATA
3049145 TT-TATA
1 TTATATA
3049151 TGTATATA
1 T-TATATA
3049159 -TATATA
1 TTATATA
3049165 -TATATA
1 TTATATA
3049171 TATATATA
1 T-TATATA
*
3049179 TTATATT
1 TTATATA
*
3049186 TTATTTA
1 TTATATA
*
3049193 TTTATTTA
1 -TTATATA
3049201 TTATA
1 TTATA
3049206 ATTTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 1 0.02
6 17 0.33
7 15 0.29
8 18 0.35
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (7 bp):
TTATATA
Found at i:3049509 original size:22 final size:21
Alignment explanation
Indices: 3049457--3049546 Score: 71
Period size: 21 Copynumber: 4.2 Consensus size: 21
3049447 CTATTTAGTA
* *
3049457 TTTTATTATATTATACATACAT
1 TTTTATTAT-TTATATATATAT
3049479 TTTTA-TATTTATATATATAT
1 TTTTATTATTTATATATATAT
*
3049499 TGTTTATTATTT-TATTTATACT
1 T-TTTATTATTTATATATATA-T
*
3049521 ATTTATTTATTT-TCAT-TATAT
1 TTTTA-TTATTTAT-ATATATAT
3049542 TTTTA
1 TTTTA
3049547 GTTTCTTTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
20 11 0.19
21 23 0.40
22 22 0.38
23 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTTATTATTTATATATATAT
Found at i:3049543 original size:28 final size:27
Alignment explanation
Indices: 3049481--3049543 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
3049471 ACATACATTT
3049481 TTATATTTATATATATATTGTTTATTA
1 TTATATTTATATATATATTGTTTATTA
* *
3049508 TTTTATTTATACTATTTATT-TATT-TTCA
1 TTATATTTATA-TATATATTGT-TTATT-A
3049536 TTATATTT
1 TTATATTT
3049544 TTAGTTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (27 bp):
TTATATTTATATATATATTGTTTATTA
Found at i:3049659 original size:20 final size:19
Alignment explanation
Indices: 3049632--3049687 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
3049622 TTTTATCTTC
3049632 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
3049651 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
3049671 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
3049688 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:3050815 original size:19 final size:19
Alignment explanation
Indices: 3050791--3050827 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3050781 ACCTTACTAA
3050791 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
3050810 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
3050828 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:3054248 original size:8 final size:8
Alignment explanation
Indices: 3054237--3054285 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 8
3054227 CAAAAAGGGC
3054237 AAAAAGAA
1 AAAAAGAA
3054245 AAAAAGAA
1 AAAAAGAA
* *
3054253 AAGAAGCA
1 AAAAAGAA
3054261 AAAAAGAA
1 AAAAAGAA
* *
3054269 GAAAACAA
1 AAAAAGAA
3054277 AAAAAGAA
1 AAAAAGAA
3054285 A
1 A
3054286 GAACAAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3054263 original size:15 final size:14
Alignment explanation
Indices: 3054238--3054294 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
3054228 AAAAAGGGCA
3054238 AAAAGAA-AAAAAG
1 AAAAGAACAAAAAG
3054251 AAAAGAAGCAAAAAAG
1 AAAAGAA-C-AAAAAG
*
3054267 AAGAA-AACAAAAAA
1 AA-AAGAACAAAAAG
3054281 AGAAAGAACAAAAA
1 A-AAAGAACAAAAA
3054295 TCAAAAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 7 0.19
14 8 0.22
15 10 0.27
16 10 0.27
17 2 0.05
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAGAACAAAAAG
Found at i:3054263 original size:16 final size:15
Alignment explanation
Indices: 3054244--3054294 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
3054234 GGCAAAAAGA
3054244 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAAGAA-C
3054260 AAAAAAGAAGAA-AAC
1 AAAAAAGAA-AAGAAC
3054275 AAAAAA-AGAAAGAAC
1 AAAAAAGA-AAAGAAC
3054290 AAAAA
1 AAAAA
3054295 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.09
15 16 0.50
16 11 0.34
17 2 0.06
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAC
Found at i:3054938 original size:22 final size:22
Alignment explanation
Indices: 3054910--3054965 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
3054900 AGCTACCCCA
3054910 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
3054932 TCAAACCTTTGAGCATCAAATG
1 TCAAACCTTTGAGCATCAAATG
3054954 -CAAAACCTTTGA
1 TC-AAACCTTTGA
3054966 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (22 bp):
TCAAACCTTTGAGCATCAAATG
Found at i:3056084 original size:106 final size:106
Alignment explanation
Indices: 3055896--3057084 Score: 1697
Period size: 106 Copynumber: 11.3 Consensus size: 106
3055886 GCCATCCGCG
* * * * ** *
3055896 ATTTCAACTCCACAACGGAGGATATCGTGCCACTCGAGACAACATAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
3055961 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
3056005 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3056070 ACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
3056111 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3056176 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCATAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
3056217 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3056282 ACCGCTGGTTTTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
** *
3056323 ATTTCAACTTCACAATAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3056388 ACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
3056429 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
3056494 ACCGCTAGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
** * *
3056535 ATTTCAACTTCACAGTGAAGGATATTGGACTCAAGAGAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3056600 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
3056641 ATTTCAACTTCA-AAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
3056705 GACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGATCCA
65 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
3056747 ATTTAAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3056812 ACCGCTGGTTGTCAATAAACAACTTCCCAA--T------C-
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * * * * * *
3056844 ---TCAACTTCACAGCGAATGATATTGTACTCGAGATAACACAAGTTCAACTTCACAACAAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3056906 A-CGACTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
66 ACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
3056947 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* ** *
3057012 A-CGTCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
3057053 ATTTCAACTTCACGACGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
3057085 GGAACAATGC
Statistics
Matches: 987, Mismatches: 78, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
93 2 0.00
94 77 0.08
96 1 0.00
98 1 0.00
102 1 0.00
104 1 0.00
105 1 0.00
106 876 0.89
107 4 0.00
109 23 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:3058388 original size:18 final size:16
Alignment explanation
Indices: 3058346--3058393 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3058336 AAAATATGAA
*
3058346 AAAAATTA-AAAAAAT
1 AAAAATTATTAAAAAT
*
3058361 AGAAATTATTAAAAAT
1 AAAAATTATTAAAAAT
3058377 AAAAATAATATTAAAAA
1 AAAAAT--TATTAAAAA
3058394 ATTTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.26
16 11 0.41
18 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAAATTATTAAAAAT
Found at i:3058389 original size:21 final size:21
Alignment explanation
Indices: 3058355--3058442 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 21
3058345 AAAAAATTAA
*
3058355 AAAAATAGAAATTATTAAAAAT
1 AAAAATA-ATATTATTAAAAAT
3058377 AAAAATAATATTA--AAAAAT
1 AAAAATAATATTATTAAAAAT
** *
3058396 TTAAA-AATATTATATAAAAGT
1 AAAAATAATATTAT-TAAAAAT
* *
3058417 ATAAATTATAAGTTATT-AAAAT
1 AAAAATAAT-A-TTATTAAAAAT
3058439 AAAA
1 AAAA
3058443 TATTAAAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 7 0.13
19 9 0.17
21 14 0.27
22 16 0.31
23 2 0.04
24 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAAATAATATTATTAAAAAT
Found at i:3058404 original size:18 final size:18
Alignment explanation
Indices: 3058332--3058421 Score: 76
Period size: 18 Copynumber: 4.8 Consensus size: 18
3058322 AAATCTATTT
*
3058332 TTAAAAAATATGAAAAAAA
1 TTAAAAAATAT-AAAAATA
*
3058351 TTAAAAAA-ATAGAAATTA
1 TTAAAAAATATA-AAAATA
*
3058369 TT-AAAAATAAAAATAATA
1 TTAAAAAATATAAA-AATA
*
3058387 TTAAAAAATTTAAAAATA
1 TTAAAAAATATAAAAATA
3058405 TTATATAAAAGTATAAA
1 TTA-A-AAAA-TATAAA
3058422 TTATAAGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.14
18 22 0.39
19 18 0.32
20 4 0.07
21 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TTAAAAAATATAAAAATA
Found at i:3058451 original size:8 final size:8
Alignment explanation
Indices: 3058438--3058462 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3058428 GTTATTAAAA
3058438 TAAAATAT
1 TAAAATAT
3058446 TAAAATAT
1 TAAAATAT
3058454 TAAAATAT
1 TAAAATAT
3058462 T
1 T
3058463 TATAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAAATAT
Found at i:3060904 original size:32 final size:32
Alignment explanation
Indices: 3060735--3060913 Score: 146
Period size: 32 Copynumber: 5.6 Consensus size: 32
3060725 TAATATCAGC
* * *
3060735 ATCGCATTCAAATAATGCATAGCAGAGTCAAT
1 ATCGCATTCAAATAATGCATAACAGAGTTAGT
* ** *
3060767 ATCACATTCAGAA-AATGCATAGTAAAGTTAGT
1 ATCGCATTCA-AATAATGCATAACAGAGTTAGT
** * * *
3060799 ATTACATTCAGATAATGCATAGA-AAAGTTGGT
1 ATCGCATTCAAATAATGCATA-ACAGAGTTAGT
* * * *
3060831 ATTGCATTTAGATAATGCATAGCAGAGTTAGT
1 ATCGCATTCAAATAATGCATAACAGAGTTAGT
3060863 ATCGCATTCAAATAATGCATAACAGAGTTAGT
1 ATCGCATTCAAATAATGCATAACAGAGTTAGT
* * * *
3060895 GTTGTATTCAGATAATGCA
1 ATCGCATTCAAATAATGCA
3060914 CAGGAGCGTC
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.01
32 118 0.98
33 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (32 bp):
ATCGCATTCAAATAATGCATAACAGAGTTAGT
Found at i:3060908 original size:64 final size:64
Alignment explanation
Indices: 3060735--3060913 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 64
3060725 TAATATCAGC
* * * ** * *
3060735 ATCGCATTCAAATAATGCATAGCAGAGTCAATATCACATTCAGAAAATGCATAGTAAAGTTAGT
1 ATCGCATTCAAATAATGCATAACAGAGTTAGTATTGCATTCAGATAATGCATAGCAAAGTTAGT
** * * * * *
3060799 ATTACATTCAGATAATGCATAGA-AAAGTTGGTATTGCATTTAGATAATGCATAGCAGAGTTAGT
1 ATCGCATTCAAATAATGCATA-ACAGAGTTAGTATTGCATTCAGATAATGCATAGCAAAGTTAGT
* *
3060863 ATCGCATTCAAATAATGCATAACAGAGTTAGTGTTGTATTCAGATAATGCA
1 ATCGCATTCAAATAATGCATAACAGAGTTAGTATTGCATTCAGATAATGCA
3060914 CAGGAGCGTC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
63 1 0.01
64 90 0.99
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (64 bp):
ATCGCATTCAAATAATGCATAACAGAGTTAGTATTGCATTCAGATAATGCATAGCAAAGTTAGT
Found at i:3060928 original size:64 final size:64
Alignment explanation
Indices: 3060730--3060930 Score: 188
Period size: 64 Copynumber: 3.1 Consensus size: 64
3060720 TATAGTAATA
* * * * ** * * *
3060730 TCAGCATCGCATTCAAATAATGCATAGCAGAGTCAATATCACATTCAGAAAATGCATAGTAAAG
1 TCAGTATCGCATTCAAATAATGCATAACAGAGTTAGTATTGCATTCAGATAATGCATAGCAGAG
* ** * * * *
3060794 TTAGTATTACATTCAGATAATGCATAGA-AAAGTTGGTATTGCATTTAGATAATGCATAGCAGAG
1 TCAGTATCGCATTCAAATAATGCATA-ACAGAGTTAGTATTGCATTCAGATAATGCATAGCAGAG
* * * * * *
3060858 TTAGTATCGCATTCAAATAATGCATAACAGAGTTAGTGTTGTATTCAGATAATGCACAGGAGCG
1 TCAGTATCGCATTCAAATAATGCATAACAGAGTTAGTATTGCATTCAGATAATGCATAGCAGAG
3060922 TCAGTATCG
1 TCAGTATCG
3060931 TATTTAGACA
Statistics
Matches: 107, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
63 1 0.01
64 106 0.99
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (64 bp):
TCAGTATCGCATTCAAATAATGCATAACAGAGTTAGTATTGCATTCAGATAATGCATAGCAGAG
Found at i:3060936 original size:96 final size:96
Alignment explanation
Indices: 3060730--3060945 Score: 227
Period size: 96 Copynumber: 2.2 Consensus size: 96
3060720 TATAGTAATA
* * * **
3060730 TCAGCATCGCATTCAAATAATGCATAGCAGAGTCAATATCACATTCAGAAAATGCATAGTAAAGT
1 TCAGTATCGCATTTAGATAATGCATAGCAGAGTCAATATCACATTCAGAAAATGCATAACAAAGT
*
3060795 TAGTATTACATTCAGATAATGCATAGAAAAG
66 TAGTATTACATTCAGATAATGCACAGAAAAG
** * * * * *
3060826 TTGGTATTGCATTTAGATAATGCATAGCAGAGTTAGTATCGCATTCA-AATAATGCATAACAGAG
1 TCAGTATCGCATTTAGATAATGCATAGCAGAGTCAATATCACATTCAGAA-AATGCATAACAAAG
* ** * **
3060890 TTAGTGTTGTATTCAGATAATGCACAGGAGCG
65 TTAGTATTACATTCAGATAATGCACAGAAAAG
* *
3060922 TCAGTATCGTATTTAGACAATGCA
1 TCAGTATCGCATTTAGATAATGCA
3060946 CATCAAATAC
Statistics
Matches: 95, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
95 2 0.02
96 93 0.98
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
TCAGTATCGCATTTAGATAATGCATAGCAGAGTCAATATCACATTCAGAAAATGCATAACAAAGT
TAGTATTACATTCAGATAATGCACAGAAAAG
Found at i:3062691 original size:15 final size:15
Alignment explanation
Indices: 3062639--3062694 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3062629 TAGTACTTTA
* *
3062639 TAAATATTTTTAAAT
1 TAAATAATTTAAAAT
*
3062654 TAGAAT-TTTTAATAAT
1 TA-AATAATTTAA-AAT
*
3062670 TATATAATTTAAAAT
1 TAAATAATTTAAAAT
3062685 TAAATAATTT
1 TAAATAATTT
3062695 CACCTTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TAAATAATTTAAAAT
Found at i:3065009 original size:42 final size:42
Alignment explanation
Indices: 3064950--3065029 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
3064940 GGGATTTCTA
* *
3064950 AATACCTGGGTTAAGGTTGTTTGGTTGCTTCTTGCATGTGAT
1 AATACCTGGGTTAAGGTTGTTCGGCTGCTTCTTGCATGTGAT
*
3064992 AATACCTGGGTTGAGGTTGTTCGGCTGCTTCTTGCATG
1 AATACCTGGGTTAAGGTTGTTCGGCTGCTTCTTGCATG
3065030 GGTGTTGCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (42 bp):
AATACCTGGGTTAAGGTTGTTCGGCTGCTTCTTGCATGTGAT
Found at i:3067182 original size:149 final size:149
Alignment explanation
Indices: 3067012--3067310 Score: 598
Period size: 149 Copynumber: 2.0 Consensus size: 149
3067002 CATAAATCAG
3067012 CAATTAATAATTAACTTTCAGCATAGACCTTCAACAATTAAGCAATTACACTTGTTACCGCAAAG
1 CAATTAATAATTAACTTTCAGCATAGACCTTCAACAATTAAGCAATTACACTTGTTACCGCAAAG
3067077 TTCCTAAAATATGCAGGATGATCCCTACACATTCACCAAGTTCCAAATTGGTCCAAACAAACTTC
66 TTCCTAAAATATGCAGGATGATCCCTACACATTCACCAAGTTCCAAATTGGTCCAAACAAACTTC
3067142 CACATAATGTAGAATCAAT
131 CACATAATGTAGAATCAAT
3067161 CAATTAATAATTAACTTTCAGCATAGACCTTCAACAATTAAGCAATTACACTTGTTACCGCAAAG
1 CAATTAATAATTAACTTTCAGCATAGACCTTCAACAATTAAGCAATTACACTTGTTACCGCAAAG
3067226 TTCCTAAAATATGCAGGATGATCCCTACACATTCACCAAGTTCCAAATTGGTCCAAACAAACTTC
66 TTCCTAAAATATGCAGGATGATCCCTACACATTCACCAAGTTCCAAATTGGTCCAAACAAACTTC
3067291 CACATAATGTAGAATCAAT
131 CACATAATGTAGAATCAAT
3067310 C
1 C
3067311 TAATATTACA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (149 bp):
CAATTAATAATTAACTTTCAGCATAGACCTTCAACAATTAAGCAATTACACTTGTTACCGCAAAG
TTCCTAAAATATGCAGGATGATCCCTACACATTCACCAAGTTCCAAATTGGTCCAAACAAACTTC
CACATAATGTAGAATCAAT
Found at i:3072388 original size:29 final size:30
Alignment explanation
Indices: 3072343--3072407 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
3072333 TAAGATTAGG
*
3072343 TTTTTACACTTAAGTCCCTAGACTTTA-TA
1 TTTTTACACTTAAGTCCATAGACTTTAGTA
* * *
3072372 TTTTTACACTTAGGTCCATGGACTTTAGTT
1 TTTTTACACTTAAGTCCATAGACTTTAGTA
3072402 TTTTTA
1 TTTTTA
3072408 TTTTAGTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (30 bp):
TTTTTACACTTAAGTCCATAGACTTTAGTA
Found at i:3074372 original size:28 final size:28
Alignment explanation
Indices: 3074322--3074379 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
3074312 AGTCTACCTT
*
3074322 CTAAGGAGACAAGCCAAATATCTAAATA
1 CTAAGGAGACAAGCCAAACATCTAAATA
* * *
3074350 CTAAGGAGACAAGTCGAACATCTACATA
1 CTAAGGAGACAAGCCAAACATCTAAATA
3074378 CT
1 CT
3074380 GAGTAAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.19
Consensus pattern (28 bp):
CTAAGGAGACAAGCCAAACATCTAAATA
Found at i:3076060 original size:21 final size:20
Alignment explanation
Indices: 3076028--3076081 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
3076018 ACACAAAGAG
*
3076028 AAAAAGAGAAAATA-TAGCAA
1 AAAAAGAAAAAATATTAG-AA
3076048 AAATAAGAAAAAATATTAGAA
1 AAA-AAGAAAAAATATTAGAA
3076069 AAAAGAGAAAAAA
1 AAAA-AGAAAAAA
3076082 AAGAGAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.13
21 23 0.77
22 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAAAGAAAAAATATTAGAA
Found at i:3076081 original size:11 final size:11
Alignment explanation
Indices: 3076067--3076129 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
3076057 AAAATATTAG
3076067 AAAAAAGAGAA
1 AAAAAAGAGAA
3076078 AAAAAAGAGAA
1 AAAAAAGAGAA
* *
3076089 AGAATAGA-AA
1 AAAAAAGAGAA
* *
3076099 GAAAAAGAAAA
1 AAAAAAGAGAA
3076110 CAAAAAAGAAGAA
1 -AAAAAAG-AGAA
3076123 AGAAAAA
1 A-AAAAA
3076130 TCATTCAAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
10 7 0.17
11 19 0.46
12 7 0.17
13 8 0.20
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:3076889 original size:29 final size:29
Alignment explanation
Indices: 3076852--3076907 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
3076842 CTTAACGAAA
3076852 AAAACCAACCT-AAGACACAT-TACCTCCCC
1 AAAACCAACCTGAA-ACAC-TCTACCTCCCC
*
3076881 AAAATCAACCTGAAACACTCTACCTCC
1 AAAACCAACCTGAAACACTCTACCTCC
3076908 ACAAGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 21 0.88
30 2 0.08
ACGTcount: A:0.41, C:0.39, G:0.04, T:0.16
Consensus pattern (29 bp):
AAAACCAACCTGAAACACTCTACCTCCCC
Found at i:3078668 original size:164 final size:161
Alignment explanation
Indices: 3078383--3078692 Score: 431
Period size: 164 Copynumber: 1.9 Consensus size: 161
3078373 GTCAAATCTA
* * * *
3078383 ATTTTTAGGGGTTTCTTGATGTCTTCAAATAAATTTTGAAAGAAACTAAGCCTAATTTTTAGGGG
1 ATTTTTAAGGGTTTCTTGATGTCTTCAAATAAATTCTGAAAAAAACTAAGCCTAATTTTCAGGGG
* * * * *
3078448 TTTCTTGATGTCTTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTTGGGGTTTCTTGATGT
66 TTTCTTGATATCTTCAAATGAATTTGGAAAGAAGCTAAACCTAATTTTTAGGGGTTTCTTGATGT
3078513 CTTCAAAGGAATTTTTAAATGAGTTAAGACT
131 CTTCAAAGGAATTTTTAAATGAGTTAAGACT
* * *
3078544 ATTTTTAAGGGTTTCTTGATGTCTTCAAATGAATTCTGAAAAAAAAAACTCAGTCTAATTTTCAG
1 ATTTTTAAGGGTTTCTTGATGTCTTCAAATAAATTCTG---AAAAAAACTAAGCCTAATTTTCAG
* * * * *
3078609 GGGTTTCTTGATATTTTCAAATGGATTTGGAAAGGAGTTAAACCTGATTTTTAGGGGTTTCTTGA
63 GGGTTTCTTGATATCTTCAAATGAATTTGGAAAGAAGCTAAACCTAATTTTTAGGGGTTTCTTGA
*
3078674 TGTCTTCAAATGAATTTTT
128 TGTCTTCAAAGGAATTTTT
3078693 GAATAAGCCA
Statistics
Matches: 128, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
161 35 0.27
164 93 0.73
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.42
Consensus pattern (161 bp):
ATTTTTAAGGGTTTCTTGATGTCTTCAAATAAATTCTGAAAAAAACTAAGCCTAATTTTCAGGGG
TTTCTTGATATCTTCAAATGAATTTGGAAAGAAGCTAAACCTAATTTTTAGGGGTTTCTTGATGT
CTTCAAAGGAATTTTTAAATGAGTTAAGACT
Found at i:3078724 original size:54 final size:54
Alignment explanation
Indices: 3078296--3078700 Score: 386
Period size: 54 Copynumber: 7.4 Consensus size: 54
3078286 ATATGATATT
* * * * * * *
3078296 TTCAAATGAATATTTTGAAATAATCTAAATCCTAATTCTCAAGGGTTTCGTGATTTC
1 TTCAAATG-A-ATTTTGAAATAAGCT-AAGCCTAATTTTTAGGGGTTTCTTGATGTC
* * **
3078353 TTCGAATG-ATTTTGAAAGAAG-TCAAATCTAATTTTTAGGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAATAAGCT-AAGCCTAATTTTTAGGGGTTTCTTGATGTC
* * *
3078406 TTCAAATAAATTTTGAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
*
3078460 TTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTTGGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
* * * * * *
3078514 TTCAAAGGAATTTTTAAATGAGTTAAGACT-ATTTTTAAGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
* * * * * * * *
3078567 TTCAAATGAATTCTGAAAAAAAAAACTCAGTCTAATTTTCAGGGGTTTCTTGATATT
1 TTCAAATGAATTTTG---AAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
* * ** * * *
3078624 TTCAAATGGATTTGGAAAGGAGTTAAACCTGATTTTTAGGGGTTTCTTGATGTC
1 TTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
3078678 TTCAAATGAATTTTTG-AATAAGC
1 TTCAAATGAA-TTTTGAAATAAGC
3078701 CAAGTTTGAT
Statistics
Matches: 282, Mismatches: 59, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
53 63 0.22
54 167 0.59
55 5 0.02
56 9 0.03
57 38 0.13
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (54 bp):
TTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTC
Found at i:3080335 original size:118 final size:118
Alignment explanation
Indices: 3080116--3080369 Score: 393
Period size: 118 Copynumber: 2.2 Consensus size: 118
3080106 GACAAATCAG
* * *
3080116 TCAACATTTTCAATGGAAGGGTTCATAATAAGAAGAACTCATCCGATGATGGAGAAAAAGTTCAT
1 TCAACATTTCCAATGAAAGGGTTCATAATAAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCAT
*
3080181 AATGAGAAGAACTTGTTCAACCTTGGTTCGAGTCCATAACAGAAGGAGGTGGA
66 AATGAGAAGAACTTGTTCAACCTTGGCTCGAGTCCATAACAGAAGGAGGTGGA
* * *
3080234 TCAACATTTCCAATGAAAGGGTAT-GTAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
1 TCAACATTTCCAATGAAAGGGT-TCATAATAAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCA
* * * *
3080298 TAATGAGAAGATCTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGGTGGA
65 TAATGAGAAGAACTTGTTCAACCTTGGCTCGAGTCCATAACAGAAGGAGGTGGA
3080352 TCAACATTTCCAATGAAA
1 TCAACATTTCCAATGAAA
3080370 ACATTCACTG
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
118 123 0.99
119 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (118 bp):
TCAACATTTCCAATGAAAGGGTTCATAATAAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTGGCTCGAGTCCATAACAGAAGGAGGTGGA
Found at i:3080395 original size:77 final size:79
Alignment explanation
Indices: 3080299--3080508 Score: 244
Period size: 78 Copynumber: 2.7 Consensus size: 79
3080289 AGAAGTTCAT
* *
3080299 AATGAGAAGATCTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTTCCA
1 AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCA
3080364 AT-GAAAACATT-C
66 ATGGAAAACATTGC
* * * * **
3080376 ACTGAGAAGAACTTGTTCAACATTTCACTTGATTCCATCACAGAATAAGATGGATCAACATTTCC
1 AATGAGAAGAACTTGTTCAACCTTT-GCTCGATTCCATCACAGAAGGAGATGGATCAACATTTCC
* ** *
3080441 AATGGAAGAGTTTGT
65 AATGGAAAACATTGC
* * * * *
3080456 AATGATAAGAAATTATTCAACCTTTGCTCGATTCCATCACATAAGGAGTTGGA
1 AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGATGGA
3080509 ACAGAACTGA
Statistics
Matches: 107, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
77 22 0.21
78 37 0.35
79 28 0.26
80 20 0.19
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (79 bp):
AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCCATCACAGAAGGAGATGGATCAACATTTCCA
ATGGAAAACATTGC
Found at i:3082392 original size:30 final size:29
Alignment explanation
Indices: 3082337--3082399 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
3082327 TTAATTACAA
* *
3082337 TTTAATCCCTAAATTATTTTATTTTTTAT
1 TTTAATCCCTAAATAATTGTATTTTTTAT
*
3082366 TTTAATCCCTAGACTAATTGTATTTTTTAT
1 TTTAATCCCTA-AATAATTGTATTTTTTAT
3082396 TTTA
1 TTTA
3082400 GCCCTCTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (29 bp):
TTTAATCCCTAAATAATTGTATTTTTTAT
Found at i:3082470 original size:29 final size:30
Alignment explanation
Indices: 3082411--3082481 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
3082401 CCCTCTAAGA
*
3082411 TTAG-ATTCTTTACGCTTAAGTCCCTATACT
1 TTAGTATT-TTTACACTTAAGTCCCTATACT
*
3082441 TT-GTATTTTTACACTTAAGTCTCTGA-ACT
1 TTAGTATTTTTACACTTAAGTCCCT-ATACT
*
3082470 TTAGTTTTTTTA
1 TTAGTATTTTTA
3082482 TTATAGTCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.51
Consensus pattern (30 bp):
TTAGTATTTTTACACTTAAGTCCCTATACT
Found at i:3087473 original size:10 final size:10
Alignment explanation
Indices: 3087458--3087496 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
3087448 AGCTCCCGAC
3087458 TTCAATTCCA
1 TTCAATTCCA
3087468 TTCAATTCCA
1 TTCAATTCCA
*
3087478 ATCAATTCCA
1 TTCAATTCCA
3087488 TATCAATTC
1 T-TCAATTC
3087497 AATCCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.38
Consensus pattern (10 bp):
TTCAATTCCA
Found at i:3087484 original size:20 final size:20
Alignment explanation
Indices: 3087459--3087500 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3087449 GCTCCCGACT
3087459 TCAATTCCAT-TCAATTCCAA
1 TCAATTCCATATCAATT-CAA
3087479 TCAATTCCATATCAATTCAA
1 TCAATTCCATATCAATTCAA
3087499 TC
1 TC
3087501 CAAAATCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (20 bp):
TCAATTCCATATCAATTCAA
Found at i:3088395 original size:29 final size:29
Alignment explanation
Indices: 3088350--3088422 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
3088340 ACCAAAATAC
* *
3088350 ACTTTTAAAATTATATT-TTTAGTCC-CTAA
1 ACTTTCAAAATT-TATTATTT-GGCCACTAA
*
3088379 ACTTTTCCAAATTTATTATTTGGCCACTAA
1 AC-TTTCAAAATTTATTATTTGGCCACTAA
3088409 ACTTTCAAAATTTA
1 ACTTTCAAAATTTA
3088423 CATTTTGGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.45
Consensus pattern (29 bp):
ACTTTCAAAATTTATTATTTGGCCACTAA
Found at i:3088429 original size:29 final size:30
Alignment explanation
Indices: 3088375--3088437 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
3088365 TTTTTAGTCC
* *
3088375 CTAAACTTTTCCAAATTTATTATTTGGCCA
1 CTAAACTTTTCAAAATTTAATATTTGGCCA
*
3088405 CTAAAC-TTTCAAAATTTACAT-TTTGGTCA
1 CTAAACTTTTCAAAATTTA-ATATTTGGCCA
3088434 CTAA
1 CTAA
3088438 CCAAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCAAAATTTAATATTTGGCCA
Found at i:3089746 original size:20 final size:20
Alignment explanation
Indices: 3089721--3089771 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
3089711 CCTATGGGGA
3089721 GTATCGATACTTTAACCTTG
1 GTATCGATACTTTAACCTTG
3089741 GTATCGATACTTTAACCTTG
1 GTATCGATACTTTAACCTTG
3089761 GTATCGATACT
1 GTATCGATACT
3089772 CCCATGAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (20 bp):
GTATCGATACTTTAACCTTG
Found at i:3090621 original size:20 final size:20
Alignment explanation
Indices: 3090558--3090621 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
3090548 TAAGCCTCTG
* *
3090558 GTATGGATACTCAATCTTT-A
1 GTATGGAAAC-CAGTCTTTCA
* * * *
3090578 GTATGGAGACCAGTCCTCCG
1 GTATGGAAACCAGTCTTTCA
3090598 GTATGGAAACCAGTCTTTCA
1 GTATGGAAACCAGTCTTTCA
3090618 GTAT
1 GTAT
3090622 AGATACTAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
GTATGGAAACCAGTCTTTCA
Found at i:3092294 original size:29 final size:29
Alignment explanation
Indices: 3092252--3092308 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
3092242 AAGAAACATT
3092252 TCTTCCCTCTCAATTGAGAACGAGGGATC
1 TCTTCCCTCTCAATTGAGAACGAGGGATC
3092281 TCTTCCCTCTCAATTGAGAACGAGGGAT
1 TCTTCCCTCTCAATTGAGAACGAGGGAT
3092309 ATTTATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (29 bp):
TCTTCCCTCTCAATTGAGAACGAGGGATC
Found at i:3094751 original size:59 final size:60
Alignment explanation
Indices: 3094668--3094782 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
3094658 GATCATATGA
* * * * * * *
3094668 ATAGTCGAGTGACTATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGCAACACTTT
1 ATAGTCGAATGACTATTTTATAACTTTCAACAGATGACACACTCAACAAAGCAACACTTT
*
3094728 ATAGTCGAATGA-TATTTTATAACTTTCAACAGATGACTCACTCAACAAAGCAACA
1 ATAGTCGAATGACTATTTTATAACTTTCAACAGATGACACACTCAACAAAGCAACA
3094783 TCCTATAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 36 0.77
60 11 0.23
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (60 bp):
ATAGTCGAATGACTATTTTATAACTTTCAACAGATGACACACTCAACAAAGCAACACTTT
Found at i:3099061 original size:123 final size:122
Alignment explanation
Indices: 3098887--3099136 Score: 349
Period size: 123 Copynumber: 2.0 Consensus size: 122
3098877 CTTACACTAT
* * * *
3098887 TAAAACATAAGTTTACATATTAAAATTGTGTTTGTAACGTTGGATTTGTTAAATAAAATTTTAAT
1 TAAAAAATAAGTTTACATATTAAAATTGTGTTTGTAACGTTAGATTCGTTAAATAAAATCTTAAT
* * *
3098952 ACAATTTTATTTTTTAAATTATAATACATATATAGTAATTTAAAAATAATTATGAAAAA
66 ACAATTTTA-TTTTTAAAATAT-ATACATATATAATAATTGAAAAATAATTATGAAAAA
* * * * *
3099011 TAAAAAATAA-TTTATATATTTAAGTTGTGTTTTTAACTTTAGATTCGTTAAATAAAATCTTAAT
1 TAAAAAATAAGTTTACATATTAAAATTGTGTTTGTAACGTTAGATTCGTTAAATAAAATCTTAAT
* *
3099075 ATAATTTTATTTTTAAAATATATTCATATATAATAATTGAAAAATAATTATGAAAAA
66 ACAATTTTATTTTTAAAATATATACATATATAATAATTGAAAAATAATTATGAAAAA
3099132 TAAAA
1 TAAAA
3099137 TTAACACAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
121 38 0.34
122 11 0.10
123 54 0.48
124 9 0.08
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (122 bp):
TAAAAAATAAGTTTACATATTAAAATTGTGTTTGTAACGTTAGATTCGTTAAATAAAATCTTAAT
ACAATTTTATTTTTAAAATATATACATATATAATAATTGAAAAATAATTATGAAAAA
Done.